data_1BJD # _entry.id 1BJD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1BJD pdb_00001bjd 10.2210/pdb1bjd/pdb WWPDB D_1000171825 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1BJD _pdbx_database_status.recvd_initial_deposition_date 1998-06-24 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Allawi, H.T.' 1 'Santalucia Junior, J.' 2 # _citation.id primary _citation.title 'NMR solution structure of a DNA dodecamer containing single G*T mismatches.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 26 _citation.page_first 4925 _citation.page_last 4934 _citation.year 1998 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9776755 _citation.pdbx_database_id_DOI 10.1093/nar/26.21.4925 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Allawi, H.T.' 1 ? primary 'SantaLucia Jr., J.' 2 ? # _cell.entry_id 1BJD _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BJD _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*CP*GP*TP*GP*AP*CP*GP*TP*TP*AP*CP*G)-3') ; _entity.formula_weight 3678.403 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DG)(DA)(DC)(DG)(DT)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTGACGTTACG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DT n 1 4 DG n 1 5 DA n 1 6 DC n 1 7 DG n 1 8 DT n 1 9 DT n 1 10 DA n 1 11 DC n 1 12 DG n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1BJD _struct_ref.pdbx_db_accession 1BJD _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1BJD A 1 ? 12 ? 1BJD 1 ? 12 ? 1 12 2 1 1BJD B 1 ? 12 ? 1BJD 1 ? 12 ? 1 12 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 COSY 1 3 1 HETCOR 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents WATER # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model UNITY _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1BJD _pdbx_nmr_refine.method 'RESTRAINED MOLECULAR DYNAMICS' _pdbx_nmr_refine.details 'RESTRAINED DISTANCES AND DIHEDRAL ANGLES' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1BJD _pdbx_nmr_details.text 'MEAN STRUCTURE. STRUCTURE WAS DETERMINED USING RELAXATION MATRIX ANALYSIS OF NOE DATA.' # _pdbx_nmr_ensemble.entry_id 1BJD _pdbx_nmr_ensemble.conformers_calculated_total_number 1 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _pdbx_nmr_representative.entry_id 1BJD _pdbx_nmr_representative.conformer_id 13 _pdbx_nmr_representative.selection_criteria ? # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR ? BRUNGER 1 'structure solution' 'VNMR FELIX' FELIX ? 2 # _exptl.entry_id 1BJD _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1BJD _struct.title ;SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING SINGLE G*T MISMATCHES USING RELAXATION MATRIX ANALYSIS AND RESTRAINED MOLECULAR DYNAMICS, NMR, 1 STRUCTURE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1BJD _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DEOXYRIBONUCLEIC ACID, DNA, G*T MISMATCH' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DT 9 O2 ? ? A DG 4 B DT 9 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DT 9 N3 ? ? A DG 4 B DT 9 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 6 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 6 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 6 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 7 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 7 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 7 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DG 4 O6 ? ? A DT 9 B DG 4 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A DT 9 O2 ? ? ? 1_555 B DG 4 N1 ? ? A DT 9 B DG 4 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 10 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 10 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1BJD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1BJD _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DA 10 10 10 DA A A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 1 1 DC C B . n B 1 2 DG 2 2 2 DG G B . n B 1 3 DT 3 3 3 DT T B . n B 1 4 DG 4 4 4 DG G B . n B 1 5 DA 5 5 5 DA A B . n B 1 6 DC 6 6 6 DC C B . n B 1 7 DG 7 7 7 DG G B . n B 1 8 DT 8 8 8 DT T B . n B 1 9 DT 9 9 9 DT T B . n B 1 10 DA 10 10 10 DA A B . n B 1 11 DC 11 11 11 DC C B . n B 1 12 DG 12 12 12 DG G B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 1999-01-13 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal VNMR 'model building' . ? 1 X-PLOR 'model building' . ? 2 X-PLOR refinement . ? 3 VNMR phasing . ? 4 X-PLOR phasing . ? 5 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 109.20 103.10 6.10 0.90 N 2 1 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? 108.69 103.10 5.59 0.90 N 3 1 "C4'" A DT 3 ? ? "C3'" A DT 3 ? ? "C2'" A DT 3 ? ? 108.60 103.10 5.50 0.90 N 4 1 "C4'" A DA 5 ? ? "C3'" A DA 5 ? ? "C2'" A DA 5 ? ? 108.85 103.10 5.75 0.90 N 5 1 "C4'" A DC 6 ? ? "C3'" A DC 6 ? ? "C2'" A DC 6 ? ? 108.89 103.10 5.79 0.90 N 6 1 "C4'" A DG 7 ? ? "C3'" A DG 7 ? ? "C2'" A DG 7 ? ? 108.85 103.10 5.75 0.90 N 7 1 "C4'" A DT 8 ? ? "C3'" A DT 8 ? ? "C2'" A DT 8 ? ? 108.71 103.10 5.61 0.90 N 8 1 "C4'" A DT 9 ? ? "C3'" A DT 9 ? ? "C2'" A DT 9 ? ? 108.85 103.10 5.75 0.90 N 9 1 "C4'" A DA 10 ? ? "C3'" A DA 10 ? ? "C2'" A DA 10 ? ? 108.71 103.10 5.61 0.90 N 10 1 "C4'" A DC 11 ? ? "C3'" A DC 11 ? ? "C2'" A DC 11 ? ? 108.61 103.10 5.51 0.90 N 11 1 "C4'" B DC 1 ? ? "C3'" B DC 1 ? ? "C2'" B DC 1 ? ? 109.18 103.10 6.08 0.90 N 12 1 "C4'" B DG 2 ? ? "C3'" B DG 2 ? ? "C2'" B DG 2 ? ? 108.66 103.10 5.56 0.90 N 13 1 "C4'" B DT 3 ? ? "C3'" B DT 3 ? ? "C2'" B DT 3 ? ? 108.59 103.10 5.49 0.90 N 14 1 "C4'" B DA 5 ? ? "C3'" B DA 5 ? ? "C2'" B DA 5 ? ? 108.84 103.10 5.74 0.90 N 15 1 "C4'" B DC 6 ? ? "C3'" B DC 6 ? ? "C2'" B DC 6 ? ? 108.86 103.10 5.76 0.90 N 16 1 "C4'" B DG 7 ? ? "C3'" B DG 7 ? ? "C2'" B DG 7 ? ? 108.81 103.10 5.71 0.90 N 17 1 "C4'" B DT 8 ? ? "C3'" B DT 8 ? ? "C2'" B DT 8 ? ? 108.72 103.10 5.62 0.90 N 18 1 "C4'" B DT 9 ? ? "C3'" B DT 9 ? ? "C2'" B DT 9 ? ? 108.82 103.10 5.72 0.90 N 19 1 "C4'" B DA 10 ? ? "C3'" B DA 10 ? ? "C2'" B DA 10 ? ? 108.71 103.10 5.61 0.90 N 20 1 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 108.56 103.10 5.46 0.90 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1BJD 'double helix' 1BJD 'b-form double helix' 1BJD 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.686 -0.428 0.262 -14.764 6.265 -1.532 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.789 -0.447 0.071 -1.817 -9.346 0.111 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DT 3 1_555 B DA 10 1_555 0.046 -0.293 0.017 4.693 -13.130 0.971 3 A_DT3:DA10_B A 3 ? B 10 ? 20 1 1 A DG 4 1_555 B DT 9 1_555 -2.590 -0.786 -0.135 -1.688 -12.550 -0.584 4 A_DG4:DT9_B A 4 ? B 9 ? 28 ? 1 A DA 5 1_555 B DT 8 1_555 0.024 -0.305 0.093 1.127 -17.147 -4.486 5 A_DA5:DT8_B A 5 ? B 8 ? 20 1 1 A DC 6 1_555 B DG 7 1_555 0.753 -0.469 -0.013 5.070 -15.968 -0.739 6 A_DC6:DG7_B A 6 ? B 7 ? 19 1 1 A DG 7 1_555 B DC 6 1_555 -0.753 -0.469 -0.012 -5.069 -15.963 -0.751 7 A_DG7:DC6_B A 7 ? B 6 ? 19 1 1 A DT 8 1_555 B DA 5 1_555 -0.024 -0.304 0.094 -1.122 -17.138 -4.483 8 A_DT8:DA5_B A 8 ? B 5 ? 20 1 1 A DT 9 1_555 B DG 4 1_555 2.591 -0.786 -0.136 1.673 -12.556 -0.587 9 A_DT9:DG4_B A 9 ? B 4 ? 28 ? 1 A DA 10 1_555 B DT 3 1_555 -0.046 -0.293 0.017 -4.685 -13.153 0.965 10 A_DA10:DT3_B A 10 ? B 3 ? 20 1 1 A DC 11 1_555 B DG 2 1_555 0.789 -0.447 0.070 1.813 -9.319 0.107 11 A_DC11:DG2_B A 11 ? B 2 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.686 -0.428 0.262 14.761 6.244 -1.536 12 A_DG12:DC1_B A 12 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.050 0.380 3.017 5.050 -4.463 38.031 1.079 0.645 2.925 -6.784 -7.676 38.602 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 11 1_555 A DT 3 1_555 B DA 10 1_555 0.165 0.490 2.966 1.452 -1.034 38.847 0.849 -0.089 2.956 -1.553 -2.182 38.886 2 AA_DG2DT3:DA10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DT 3 1_555 B DA 10 1_555 A DG 4 1_555 B DT 9 1_555 0.113 0.215 2.963 -1.314 11.181 32.335 -1.257 -0.383 2.871 19.359 2.275 34.190 3 AA_DT3DG4:DT9DA10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DT 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.611 0.891 3.082 -4.598 -0.033 52.558 1.004 0.404 3.121 -0.037 5.182 52.744 4 AA_DG4DA5:DT8DT9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DA 5 1_555 B DT 8 1_555 A DC 6 1_555 B DG 7 1_555 0.088 0.557 3.037 0.225 -4.724 42.651 1.193 -0.100 2.962 -6.470 -0.308 42.900 5 AA_DA5DC6:DG7DT8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A DC 6 1_555 B DG 7 1_555 A DG 7 1_555 B DC 6 1_555 0.000 0.224 3.257 -0.007 9.935 34.947 -1.040 -0.001 3.200 16.144 0.011 36.289 6 AA_DC6DG7:DC6DG7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A DG 7 1_555 B DC 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.088 0.556 3.037 -0.219 -4.713 42.644 1.192 0.100 2.962 -6.457 0.300 42.892 7 AA_DG7DT8:DA5DC6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A DT 8 1_555 B DA 5 1_555 A DT 9 1_555 B DG 4 1_555 0.611 0.891 3.082 4.599 -0.053 52.568 1.006 -0.405 3.121 -0.059 -5.182 52.755 8 AA_DT8DT9:DG4DA5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A DT 9 1_555 B DG 4 1_555 A DA 10 1_555 B DT 3 1_555 -0.113 0.214 2.962 1.316 11.199 32.334 -1.259 0.384 2.870 19.388 -2.278 34.194 9 AA_DT9DA10:DT3DG4_BB A 9 ? B 4 ? A 10 ? B 3 ? 1 A DA 10 1_555 B DT 3 1_555 A DC 11 1_555 B DG 2 1_555 -0.165 0.490 2.966 -1.448 -1.054 38.844 0.852 0.089 2.957 -1.584 2.176 38.884 10 AA_DA10DC11:DG2DT3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.050 0.380 3.016 -5.050 -4.449 38.034 1.076 -0.646 2.925 -6.762 7.675 38.603 11 AA_DC11DG12:DC1DG2_BB A 11 ? B 2 ? A 12 ? B 1 ? #